The latest version of Flowjo is 10.1.1 - it runs on both Macs and PCs. It can be obtained from here for Mac, and here for Windows. This version is compatble with OSX 10.11 El Capitan. Flowjo requires Java 6; if you do not have it on your computer, Flowjo will prompt you to download it.
The Mac only version will no longer be developed. However, v9.9 still can be obtained from the above link for Mac.
Mac OSX v10.x has a new default that restricts downloads only from the Apple App store. You will need to go to Apple Menu > System Preferences > Security, and change the option to allow programs downloaded from Anywhere.
In your Data Archive, you can see .jo and .wsp files for each experiment. If your experiment was run before 12/15/13, download the .jo file and drop it on a blank workspace in FlowJo X; it will ask you for the login to the Data Archive and download the data to your workspace. If it was run after 12/15/13, download the .wsp file and drop it on a blank workspace to get your data from the archive. Save the .wsp workspace you have created and you will not need to do any more drag/drop of files.
FlowJo support can be obtined from: firstname.lastname@example.org; (800)366-6045. You can also use the Contact form available on this web site to ask FACS staff your question.
FlowJo, Inc. maintains a number of helpful online resources, including videos and tutorials with demo data. Please go to their web site and look at the Learning link. FlowJo application specialists also host a blog containing flowjo-related useful hints and obscuritiesl; visit The Daily Dongle link.